In my first take on the news of the FDA finalizing its request to agriculture to stop using growth-promoter antibiotics, I promised to come back for a more thoughtful reaction. And then this happened, and this happened, and the holidays happened, and, well, it’s been a busy few weeks.

So, finally getting back to it: When the news broke, a number of people, including me, said that this was a long-awaited first step on the part of the FDA, but of uncertain ultimate impact because it asks for voluntary action and does not address whether the drugs simply can be relabeled. I still agree with both those points, but think the possibly most important issue — which I raised briefly in the first post — is that merely removing antibiotics, without changing the system in which those antibiotics have been administered, may cause significant animal-welfare problems, without having any real effect on human health.

Two important, linked publications are out today, both carrying the same message: The way we raise poultry in this country is creating an under-appreciated health hazard, and the government structures we depend upon to detect that hazard and protect us from it are failing us.

The two pubs are:

A long piece that will be in the Feb. 2014 edition of Consumer Reports but has been placed online today.

Short version: Independent tests show that multi-drug resistant disease-causing bacteria are widely present on chicken, and the US Department of Agriculture’s Food Safety and Inspection Service (FSIS) has insufficient personnel, or legal authority, to change that.

It’s worth emphasizing also that we are right now in the middle of an outbreak of Salmonella on chicken that has been going on for about a year. The Centers for Disease Control and Prevention posted an update just this morning: 416 people since since last February, in 23 states and Puerto Rico, 39 percent of them hospitalized, linked to a single producer’s brand of chicken.

This is an ICYMI (“in case you missed it”) post, twice over. Last week, former Food and Drug Administration Commissioner Donald Kennedy, Ph.D., wrote a piece for the Washington Post in which he urged that the FDA change how it regulates antibiotics that are used in agriculture as part of meat production.

His prescription is notable, not just in itself, but because it marks the second time in a few months that a former commissioner of the FDA used a major paper’s op-ed page to criticize his former agency’s conduct on farm antibiotic use. David A. Kessler, M.D., did the same thing, hitting many of the same points, in the New York Times in March.

Kennedy was FDA Commissioner from 1977 to 1979, just as scrutiny of antibiotic use in livestock-raising was beginning. (There’s a timeline in this post.) Kessler was Commissioner from 1990 to 1997, during the time in which the FDA began to look for, and find, antibiotic-resistant bacteria on retail meat. There were almost 20 years between their tenures — and 16 years from Kessler to now — and yet almost nothing has changed.

In the long back and forth between science and agriculture over the source of antibiotic resistance in humans — Due to antibiotic overuse on farms, or in human medicine? — one question has been stubbornly hard to answer. If antibiotic-resistant bacteria do arise on farms, do they leave the farm and circulate in the wider world? And if they do, how much damage do they do?

A multi-national team of researchers recently published their answers to both questions. Their answer: In Europe, 1,518 deaths and 67,236 days in the hospital, every year, which would not otherwise have occurred.

In my last post I promised to catch up on some of the other research that has been published on the flow of MRSA (and other resistant organisms) between farm animals and farm workers as a result of farm antibiotic use.

Before I do that, though, I want to nod toward two other great pieces published on this. First, Mark Bittman examined this issue closely at the New York Times. And Clare Leschin-Hoar also covered the new research at Take Part. (Bonus: Don’t miss her dissection of the news that a National Geographic photographer was arrested in Kansas after taking pictures of a feedlot — from the air.)

I saved this post until today to allow everyone to get their holiday hot dogs guilt-free. Now that’s over: An important study has just been published which makes a close connection between the emergence of antibiotic-resistant bacteria, and the use of antibiotics on large-scale conventional hog farms. Bonus: It involves the resistant bacterium MRSA ST398 (known in shorthand as “pig MRSA”), which is widespread in Europe but up to this point has been found mainly in only one state in the US, Iowa. With this paper, the count rises to two(see Update): The study subjects in this paper are hog-farm workers in eastern North Carolina.

A quick explanation of why this is important: “Pig MRSA” is a particular strain of drug-resistant staph that is slightly different from the hospital and community (sports, gym) varieties. It was first spotted in the Netherlands in 2004, in the toddler daughter of pig farmers and in the family’s pigs. Since then, it has spread widely across Europe, not just in agriculture, but in healthcare and in everyday life, and has also been found widely in retail meat.

The question of whether livestock production’s use of antibiotics causes antibiotic-resistant bacteria to move into the wider world is much argued-over, and pig MRSA, or ST398 to be polite, is crucial to that dispute. That’s because, unlike most resistant bacteria, it has a genetic signature that makes an inarguable link back to farm drug use. More on that below. (If you want more, here’s an archive of my posts on ST398; the story of its emergence in 2004 and what happened afterward is told in my 2010 book SUPERBUG.)

Now, the study. Quick summary, with more unpacking to follow: Researchers checked livestock-farm workers in North Carolina to see whether they were carrying staph, and also drug-resistant staph. The workers formed two groups: one group worked at conventional hog operations, which routinely use antibiotics, and the other group at antibiotic-free farms. Both groups carried staph and also drug-resistant staph, which would be expected; about 30 percent of the population carries sensitive staph and about 4 percent carries the drug-resistant form. But, the key difference: Workers from the conventional, antibiotic-using farms were many times more likely to carry staph with the specific signature of farm-drug use.

That illuminates a potential occupational risk to the workers — and it also suggests that the workers could be a channel for that farm-influenced bacterium to move off the farm.

Quick post today as I’m getting ready for some travel. Just to note: The G8 summit is beginning in Ireland, and there is a push on to put intensive agriculture and its antibiotic use on the agenda for discussion by the major Western economies.

OK, still catching up. Today: food, foodborne illness, and antibiotic use and resistance in food — lots of news in a multi-item rundown. (Under normal circumstances, I’d give each of these items a post of its own; but since they all happened in the past few weeks, it seems better to note them and move on.)

I don’t often recommend print magazines here, because I figure they already have their own megaphone, and whatever power we at Wired have to push along other writers, I’d rather use to promote bloggers who might not have high traffic. That said: There is a piece in the currentHarper’s which should be a must-read for anyone interested in livestock agriculture and meat production in America, written by long-time immersive journalist and NYU professor Ted Conover. It is entirely behind a paywall, and so (to my perception) is not being talked about — but it should be. It is a detailed and unbiased account of how large-scale slaughter happens, and it makes some important points about routine antibiotic use.

The antibiotic era was barely 20 years old when people started raising concerns about using the new “miracle drugs” in agriculture. Penicillin first entered use in 1943, streptomycin in 1944, tetracycline in 1948 — and by 1965, the United Kingdom’s Agricultural Research Council was hearing testimony that organisms common in food animals, especially Salmonella, were becoming resistant to the antibiotics being used on the animals while they were alive. By 1969, the UK government had compiled an official report outlining the danger, and by 1973, a task force of the US Food and Drug Administration had concurred, and concluded the only safe action was to withdraw approval to use antibiotics in animals. (At which, as we now know, they would never be successful.)

The policy difficulty regarding this long-recognized problem has never been the emergence of resistant bacteria on farms; no one seriously disputes that resistance emerges whenever antibiotics exert selective pressure on bacteria, killing the vulnerable and opening an ecological niche into which the surviving not-vulnerable can expand. The sticking point has been the difficulty of proving that those resistant bacteria depart from farms, cross to humans, and cause resistant illness in them. Stuart Levy demonstrated it in 1976, on an experimental farm plot he set up just to make the proof. Most of the rest of the research, though — and after decades, there are hundreds of pieces of research — has been observational and retrospective: Looking at the drugs administered to populations of animals (about which we have very little data), measuring the antibiotic-resistant illness that arises in the human population, and making increasingly sophisticated backward matches between the resistance factors that show up in humans and the drugs that are deployed primarily on farms.

Demonstrating the bacterial traffic prospectively and experimentally, as Levy did, is challenging not just logistically but also ethically. It is difficult to imagine a study design that could trace specific animals, their meat, and their eaters in a large group of free-living humans; and unless you have volunteers, as Levy did, the study would push ethical boundaries as well. But having that lack of definition in the middle of the animal-to-human bacterial flow permits uncertainty — which proponents of continued ag antibiotic use exploit.

A new study of Danish farmers and their livestock may have ended that uncertainty. It is still retrospective, but its observations — using whole-genome sequencing — are so fine-grained that their tracing of the bacterial traffic seems to me to be difficult to challenge.